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Protein

Pyridoxine/pyridoxamine 5'-phosphate oxidase 1, chloroplastic

Gene

PPOX1

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the oxidation of either pyridoxine 5'-phosphate (PNP) or pyridoxamine 5'-phosphate (PMP) into pyridoxal 5'-phosphate (PLP). Involved in the PLP salvage pathway. Has a higher preference for PNP over PMP. May also catalyze the epimerization of the S- and R-forms of NAD(P)HX, a damaged form of NAD(P)H that is a result of enzymatic or heat-dependent hydration. This is a prerequisite for the S-specific NAD(P)H-hydrate dehydratase to allow the repair of both epimers of NAD(P)HX.2 Publications

Catalytic activityi

Pyridoxamine 5'-phosphate + H2O + O2 = pyridoxal 5'-phosphate + NH3 + H2O2.2 Publications
Pyridoxine 5'-phosphate + O2 = pyridoxal 5'-phosphate + H2O2.
(R)-NADHX = (S)-NADHX.

Cofactori

Protein has several cofactor binding sites:
  • FMNBy similarityNote: Binds 1 FMN per subunit.By similarity
  • K+By similarityNote: Binds 1 potassium ion per subunit.By similarity

Pathwayi: pyridoxal 5'-phosphate salvage

This protein is involved in step 1 of the subpathway that synthesizes pyridoxal 5'-phosphate from pyridoxamine 5'-phosphate.
Proteins known to be involved in this subpathway in this organism are:
  1. Pyridoxine/pyridoxamine 5'-phosphate oxidase 2 (PPOX2), Pyridoxine/pyridoxamine 5'-phosphate oxidase 1, chloroplastic (PPOX1)
This subpathway is part of the pathway pyridoxal 5'-phosphate salvage, which is itself part of Cofactor metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes pyridoxal 5'-phosphate from pyridoxamine 5'-phosphate, the pathway pyridoxal 5'-phosphate salvage and in Cofactor metabolism.

Pathwayi: pyridoxal 5'-phosphate salvage

This protein is involved in step 1 of the subpathway that synthesizes pyridoxal 5'-phosphate from pyridoxine 5'-phosphate.
Proteins known to be involved in this subpathway in this organism are:
  1. Pyridoxine/pyridoxamine 5'-phosphate oxidase 2 (PPOX2), Pyridoxine/pyridoxamine 5'-phosphate oxidase 1, chloroplastic (PPOX1)
This subpathway is part of the pathway pyridoxal 5'-phosphate salvage, which is itself part of Cofactor metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes pyridoxal 5'-phosphate from pyridoxine 5'-phosphate, the pathway pyridoxal 5'-phosphate salvage and in Cofactor metabolism.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi132PotassiumBy similarity1
Metal bindingi196PotassiumBy similarity1
Binding sitei238NAD(P)HXBy similarity1
Metal bindingi241PotassiumBy similarity1
Binding sitei379Pyridoxal 5'-phosphateBy similarity1
Binding sitei418FMNBy similarity1
Binding sitei436Pyridoxal 5'-phosphateBy similarity1
Binding sitei440Pyridoxal 5'-phosphateBy similarity1
Binding sitei444Pyridoxal 5'-phosphateBy similarity1
Binding sitei499FMNBy similarity1
Binding sitei509FMNBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi374 – 377FMNBy similarity4
Nucleotide bindingi389 – 390FMNBy similarity2
Nucleotide bindingi395 – 396FMNBy similarity2
Nucleotide bindingi453 – 454FMNBy similarity2

GO - Molecular functioni

  • FMN binding Source: InterPro
  • metal ion binding Source: UniProtKB-KW
  • NADHX epimerase activity Source: TAIR
  • NADPHX epimerase activity Source: TAIR
  • pyridoxamine-phosphate oxidase activity Source: TAIR

GO - Biological processi

  • NADH metabolic process Source: TAIR
  • NADP metabolic process Source: TAIR
  • pyridoxine biosynthetic process Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Isomerase, Oxidoreductase

Keywords - Biological processi

Pyridoxine biosynthesis

Keywords - Ligandi

Flavoprotein, FMN, Metal-binding, NAD, Nucleotide-binding, Potassium

Enzyme and pathway databases

BioCyciARA:AT5G49970-MONOMER.
MetaCyc:MONOMER-17901.
BRENDAi5.1.99.6. 399.
ReactomeiR-ATH-197264. Nicotinamide salvaging.
UniPathwayiUPA01068; UER00304.
UPA01068; UER00305.

Names & Taxonomyi

Protein namesi
Recommended name:
Pyridoxine/pyridoxamine 5'-phosphate oxidase 1, chloroplastic
Short name:
AtPPOX1
Including the following 2 domains:
Pyridoxine/pyridoxamine 5'-phosphate oxidase (EC:1.4.3.52 Publications)
Alternative name(s):
PNP/PMP oxidase
Short name:
PNPOx
Pyridoxal 5'-phosphate synthase
Probable NAD(P)HX epimerase (EC:5.1.99.-)
Gene namesi
Name:PPOX1
Synonyms:PDX3, PDXH
Ordered Locus Names:At5g49970
ORF Names:K9P8.11
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 5

Organism-specific databases

TAIRiAT5G49970.

Subcellular locationi

GO - Cellular componenti

  • chloroplast Source: TAIR
  • cytosol Source: TAIR
  • mitochondrion Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Chloroplast, Plastid

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Transit peptidei1 – 64ChloroplastCombined sourcesAdd BLAST64
ChainiPRO_000042054965 – 530Pyridoxine/pyridoxamine 5'-phosphate oxidase 1, chloroplasticAdd BLAST466

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei65N-acetylmethionineCombined sources1

Keywords - PTMi

Acetylation

Proteomic databases

PaxDbiQ9LTX3.

Expressioni

Tissue specificityi

Expressed in leaves, stems, flowers and roots.1 Publication

Inductioni

Circadian regulation. Up-regulated by light, heat, jasmonic acid, ethylene and abscisic acid treatments. Down-regulated by drought and salt treatment. Not induced by UV irradiation.1 Publication

Gene expression databases

GenevisibleiQ9LTX3. AT.

Interactioni

Subunit structurei

Homodimer.By similarity

Protein-protein interaction databases

STRINGi3702.AT5G49970.1.

Structurei

3D structure databases

ProteinModelPortaliQ9LTX3.
SMRiQ9LTX3.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini81 – 297YjeF N-terminalAdd BLAST217

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni131 – 135NAD(P)HXBy similarity5
Regioni200 – 206NAD(P)HXBy similarity7
Regioni247 – 250Pyridoxal 5'-phosphate bindingBy similarity4
Regioni321 – 324Substrate bindingBy similarity4
Regioni325 – 327Pyridoxal 5'-phosphate bindingBy similarity3
Regioni505 – 507Pyridoxal 5'-phosphate bindingBy similarity3

Domaini

Most plant PPOX proteins have both a pyridoxamine 5'-phosphate oxidase domain and an extra YjeF N-terminal domain.

Sequence similaritiesi

In the N-terminal section; belongs to the NnrE/AIBP family.Curated
In the C-terminal section; belongs to the pyridoxamine 5'-phosphate oxidase family.Curated
Contains 1 YjeF N-terminal domain.Curated

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiKOG2585. Eukaryota.
KOG2586. Eukaryota.
COG0062. LUCA.
COG0259. LUCA.
HOGENOMiHOG000243404.
KOiK00275.
K17759.
OMAiSESENYF.
OrthoDBiEOG093606VO.
PhylomeDBiQ9LTX3.

Family and domain databases

Gene3Di2.30.110.10. 1 hit.
3.40.50.10260. 1 hit.
HAMAPiMF_01966. NADHX_epimerase. 1 hit.
MF_01629. PdxH. 1 hit.
InterProiIPR000659. Pyridox_Oxase.
IPR019740. Pyridox_Oxase_CS.
IPR011576. Pyridox_Oxase_FMN-bd.
IPR021198. Pyridox_Oxase_pln.
IPR019576. Pyridoxamine_oxidase_dimer_C.
IPR012349. Split_barrel_FMN-bd.
IPR004443. YjeF_N_dom.
IPR032976. YJEFN_prot_eukaryotes.
[Graphical view]
PANTHERiPTHR13232. PTHR13232. 1 hit.
PfamiPF10590. PNPOx_C. 1 hit.
PF01243. Pyridox_oxidase. 1 hit.
PF03853. YjeF_N. 1 hit.
[Graphical view]
PIRSFiPIRSF037048. PyrdxN_5-P_Oxase_ross-cont_pln. 1 hit.
SUPFAMiSSF50475. SSF50475. 1 hit.
SSF64153. SSF64153. 1 hit.
TIGRFAMsiTIGR00558. pdxH. 1 hit.
TIGR00197. yjeF_nterm. 1 hit.
PROSITEiPS01064. PYRIDOX_OXIDASE. 1 hit.
PS51385. YJEF_N. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9LTX3-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MRNVIRRVTT MTFTFLLQSP PLPISPSPPQ FSLSSSPLSK TQRFITPSQG
60 70 80 90 100
SRLRTLCTKV IIPNMQDSGS PPLSYLTQRE AAEIDETLMG PLGFSIDQLM
110 120 130 140 150
ELAGLSVAAS IAEVYKPEEY SRVLAICGPG NNGGDGLVAA RHLHHFGYKP
160 170 180 190 200
FICYPKRTAK PLYTGLVTQL DSLSVPFVSV EDLPDDLSKD FDVIVDAMFG
210 220 230 240 250
FSFHGAPRPP FDDLIRRLVS LQNYEQTLQK HPVIVSVDIP SGWHVEEGDH
260 270 280 290 300
EDGGIKPDML VSLTAPKLCA KRFRGPHHFL GGRFVPPSVA EKYKLELPSY
310 320 330 340 350
PGTSMCVRIG KPPKVDISAM RVNYVSPELL EEQVETDPTV QFRKWFDEAV
360 370 380 390 400
AAGLRETNAM ALSTANKDKK PSSRMVLLKG FDENGFVWFT NYESKKGSDL
410 420 430 440 450
SENPSAALLF YWEILNRQVR IEGPVERIPE SESENYFHSR PRGSQIGAIV
460 470 480 490 500
SKQSSVVPGR HVLYDEYEEL TKQYSDGSVI PKPKNWGGFR LKPNLFEFWQ
510 520 530
GQPSRLHDRL QYSLQDVNGN PAWKIHRLAP
Length:530
Mass (Da):59,376
Last modified:October 1, 2000 - v1
Checksum:i22E8DFEC1A2167EE
GO
Isoform 2 (identifier: Q9LTX3-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     261-271: Missing.
     478-530: Missing.

Note: Not detected in roots.
Show »
Length:466
Mass (Da):52,042
Checksum:i3E2B851F982461E5
GO

Sequence cautioni

The sequence AAM65907 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence AAM83249 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti241S → Y in AAM65907 (Ref. 4) Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_044534261 – 271Missing in isoform 2. CuratedAdd BLAST11
Alternative sequenceiVSP_044535478 – 530Missing in isoform 2. CuratedAdd BLAST53

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB024032 Genomic DNA. Translation: BAA97018.1.
CP002688 Genomic DNA. Translation: AED95879.1.
CP002688 Genomic DNA. Translation: AED95878.1.
AY127025 mRNA. Translation: AAM83249.1. Different initiation.
BT000605 mRNA. Translation: AAN18174.1.
AY088368 mRNA. Translation: AAM65907.1. Different initiation.
RefSeqiNP_568717.2. NM_124376.4. [Q9LTX3-1]
NP_974918.1. NM_203189.2. [Q9LTX3-2]
UniGeneiAt.28155.

Genome annotation databases

EnsemblPlantsiAT5G49970.1; AT5G49970.1; AT5G49970. [Q9LTX3-1]
GeneIDi835061.
GrameneiAT5G49970.1; AT5G49970.1; AT5G49970.
KEGGiath:AT5G49970.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB024032 Genomic DNA. Translation: BAA97018.1.
CP002688 Genomic DNA. Translation: AED95879.1.
CP002688 Genomic DNA. Translation: AED95878.1.
AY127025 mRNA. Translation: AAM83249.1. Different initiation.
BT000605 mRNA. Translation: AAN18174.1.
AY088368 mRNA. Translation: AAM65907.1. Different initiation.
RefSeqiNP_568717.2. NM_124376.4. [Q9LTX3-1]
NP_974918.1. NM_203189.2. [Q9LTX3-2]
UniGeneiAt.28155.

3D structure databases

ProteinModelPortaliQ9LTX3.
SMRiQ9LTX3.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi3702.AT5G49970.1.

Proteomic databases

PaxDbiQ9LTX3.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT5G49970.1; AT5G49970.1; AT5G49970. [Q9LTX3-1]
GeneIDi835061.
GrameneiAT5G49970.1; AT5G49970.1; AT5G49970.
KEGGiath:AT5G49970.

Organism-specific databases

TAIRiAT5G49970.

Phylogenomic databases

eggNOGiKOG2585. Eukaryota.
KOG2586. Eukaryota.
COG0062. LUCA.
COG0259. LUCA.
HOGENOMiHOG000243404.
KOiK00275.
K17759.
OMAiSESENYF.
OrthoDBiEOG093606VO.
PhylomeDBiQ9LTX3.

Enzyme and pathway databases

UniPathwayiUPA01068; UER00304.
UPA01068; UER00305.
BioCyciARA:AT5G49970-MONOMER.
MetaCyc:MONOMER-17901.
BRENDAi5.1.99.6. 399.
ReactomeiR-ATH-197264. Nicotinamide salvaging.

Miscellaneous databases

PROiQ9LTX3.

Gene expression databases

GenevisibleiQ9LTX3. AT.

Family and domain databases

Gene3Di2.30.110.10. 1 hit.
3.40.50.10260. 1 hit.
HAMAPiMF_01966. NADHX_epimerase. 1 hit.
MF_01629. PdxH. 1 hit.
InterProiIPR000659. Pyridox_Oxase.
IPR019740. Pyridox_Oxase_CS.
IPR011576. Pyridox_Oxase_FMN-bd.
IPR021198. Pyridox_Oxase_pln.
IPR019576. Pyridoxamine_oxidase_dimer_C.
IPR012349. Split_barrel_FMN-bd.
IPR004443. YjeF_N_dom.
IPR032976. YJEFN_prot_eukaryotes.
[Graphical view]
PANTHERiPTHR13232. PTHR13232. 1 hit.
PfamiPF10590. PNPOx_C. 1 hit.
PF01243. Pyridox_oxidase. 1 hit.
PF03853. YjeF_N. 1 hit.
[Graphical view]
PIRSFiPIRSF037048. PyrdxN_5-P_Oxase_ross-cont_pln. 1 hit.
SUPFAMiSSF50475. SSF50475. 1 hit.
SSF64153. SSF64153. 1 hit.
TIGRFAMsiTIGR00558. pdxH. 1 hit.
TIGR00197. yjeF_nterm. 1 hit.
PROSITEiPS01064. PYRIDOX_OXIDASE. 1 hit.
PS51385. YJEF_N. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPPOX1_ARATH
AccessioniPrimary (citable) accession number: Q9LTX3
Secondary accession number(s): F4K7H2, Q8L7T7, Q8L9L3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 9, 2013
Last sequence update: October 1, 2000
Last modified: November 30, 2016
This is version 120 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Miscellaneous

Mutants with reduced expression of PPOX1 (RNAi) have lower levels of total B6 vitamers, a reduced growth and are sensitive to high light.1 Publication

Keywords - Technical termi

Complete proteome, Multifunctional enzyme, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.